Data cleaning and pre-processing
This section shows the main steps that have been applied to pre-process the raw data.
aCDOM spectra
The CDOM spectra were modelled according to the information in @.
acdom spectra were re-fitted using the complete data (i.e. between 350-500 nm) because the data in all_abs_transpose.txt started at 380 nm.
Average background values calculated between 683-687 nm and subtracted from each spectrum.
Some files were in binary format, so I could not open them (ex.: C2001000.YSA).
Some spectra start at 300 nm while others at 350 nm.
Calculated the correlation between the measured and the fitted values.
- Fits with R2 lower than 0.95 were removed from the data.
Absorption spectra with any negative values below 500 nm were removed.
Exported the complete spectra (350-700 nm): both the raw and the modelled data.
Phytoplankton and non-algal absorption
- Absorption spectra with any negative values below 500 nm were removed.
Irradiance
There were negative values in the irradiance data (Ed, Eu, Kd, Ku). I have cleaned the data by setting these negative values to NA.
Eu is in fact Eu0- that was estimated using a two-exponential function model.
Ed is in fact Ed0- calculated from 0.94 x ed0+.
There are differences in wavelengths among cruises. I have not found any information in the report concerning channel change across the missions.
| A2 |
C1 |
C3 |
C4 |
C5 |
C6 |
| 411 |
411 |
411 |
411 |
411 |
411 |
| 443 |
443 |
443 |
443 |
443 |
443 |
| 456 |
456 |
456 |
456 |
456 |
456 |
| 490 |
490 |
490 |
490 |
490 |
490 |
| 509 |
509 |
509 |
509 |
509 |
509 |
| 532 |
532 |
532 |
532 |
532 |
532 |
| 559 |
556 |
559 |
559 |
559 |
559 |
| 619 |
590 |
619 |
619 |
619 |
619 |
| 665 |
665 |
665 |
665 |
665 |
665 |
| 683 |
683 |
683 |
683 |
683 |
683 |
| 705 |
705 |
705 |
705 |
705 |
705 |
| 779 |
779 |
779 |
779 |
779 |
779 |
| 866 |
866 |
866 |
866 |
866 |
866 |
| A2 |
C1 |
C3 |
C4 |
C5 |
C6 |
| 559 |
556 |
559 |
559 |
559 |
559 |
| 619 |
590 |
619 |
619 |
619 |
619 |
Reflectance
- Reflectance values outside the 0-1 range were set to
NA.
Other stuff
- Extracted extra variables (
DOC, AQY) from Massimo 2000.
Bathymetry
- I have extracted the bathymetry at each sampling locations.
TODO
Use piggyback https://docs.ropensci.org/piggyback/
Release the final report PDF with a DOI and cite it in the main text.
- Who should be included in the release of this document?
Make sure that SPMR units are OK. um vs nm. Change accordingly in the SPMR code file (zzz_radiometer.R).
Remove Almofront (A2, Med case 1) observations? Looks like these were from a separate mission with different funding. Wait for Marcel’s answer.